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Bioinformatics Advance Access originally published online on September 27, 2006
Bioinformatics 2006 22(22):2821-2822; doi:10.1093/bioinformatics/btl493
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CAPS: coevolution analysis using protein sequences

Mario A. Fares * and David McNally

Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland

*To whom correspondence should be addressed.

Summary: Coevolution Analysis using Protein Sequences (CAPS) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites. Friendly interpretable output files are generated.

Availability: CAPS version 1 is available at http://bioinf.gen.tcd.ie/~faresm/software/caps/. Distribution versions for Linux/Unix, Mac OS X and Windows operating systems are available, including manual and example files.

Contact: faresm{at}tcd.ie

Received on August 11, 2006; revised on September 12, 2006; accepted on September 19, 2006

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